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-   -   problem with running in parallel (https://www.cfd-online.com/Forums/openfoam/94245-problem-running-parallel.html)

dhruv November 10, 2011 04:06
problem with running in parallel
 
Hello All,

I am having a problem with running a case in parallel. I am trying to run the case on 4 cores, with porousSimpleFoam as my solver. I am getting the following error. The case is getting decomposed, and also runs potentialFoam. But as soon as it starts the calculation, then, I get this error. I tried to run it not in parallel, and it works perfectly. I tried to check with one of my other case of porousSimpleFoam, and that works too, in parallel and in series. I don't understand the problem.

Quote:

1. Teil der Rechnung läuft ...
[1] #0 Foam::error::printStack(Foam::Ostream&)[3] #0 Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam200/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #1 Foam::sigSegv::sigHandler(int) in "/opt/openfoam200/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #2 in "/lib/libc.so.6"
[1] #3 Foam::processorPolyPatch::updateMesh(Foam::Pstream Buffers&) in "/opt/openfoam200/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #4 Foam::polyBoundaryMesh::updateMesh() in "/opt/openfoam200/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #5 Foam::polyMesh::polyMesh(Foam::IOobject const&) in "/opt/openfoam200/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[1] #6 Foam::fvMesh::fvMesh(Foam::IOobject const&) in "/opt/openfoam200/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
[1] #7
[1] in "/opt/openfoam200/platforms/linux64GccDPOpt/bin/porousSimpleFoam"
[1] #8 __libc_start_main in "/lib/libc.so.6"
[1] #9
[1] in "/opt/openfoam200/platforms/linux64GccDPOpt/bin/porousSimpleFoam"
[PCDESZR100998:06609] *** Process received signal ***
[PCDESZR100998:06609] Signal: Segmentation fault (11)
[PCDESZR100998:06609] Signal code: (-6)
[PCDESZR100998:06609] Failing at address: 0x3eb000019d1
[PCDESZR100998:06609] [ 0] /lib/libc.so.6(+0x33af0) [0x7fd6bf9e2af0]
[PCDESZR100998:06609] [ 1] /lib/libc.so.6(gsignal+0x35) [0x7fd6bf9e2a75]
[PCDESZR100998:06609] [ 2] /lib/libc.so.6(+0x33af0) [0x7fd6bf9e2af0]
[PCDESZR100998:06609] [ 3] /opt/openfoam200/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam18processorPolyPatch10updat eMeshERNS_14PstreamBuffersE+0x2e6) [0x7fd6c09991e6]
[PCDESZR100998:06609] [ 4] /opt/openfoam200/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam16polyBoundaryMesh10updateM eshEv+0x2b1) [0x7fd6c09a0211]
[PCDESZR100998:06609] [ 5] /opt/openfoam200/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZN4Foam8polyMeshC2ERKNS_8IOobjectE +0x1042) [0x7fd6c09f10f2]
[PCDESZR100998:06609] [ 6] /opt/openfoam200/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam6fvMeshC1ERKNS_8IOobjec tE+0x19) [0x7fd6c15e5119]
[PCDESZR100998:06609] [ 7] porousSimpleFoam() [0x41c9e3]
[PCDESZR100998:06609] [ 8] /lib/libc.so.6(__libc_start_main+0xfd) [0x7fd6bf9cdc4d]
[PCDESZR100998:06609] [ 9] porousSimpleFoam() [0x41a269]
[PCDESZR100998:06609] *** End of error message ***
Does anyone have an idea???

Regards,
Dhruv.

danishdude November 10, 2011 10:33
More Information Needed
 
Can you give us the top part of the error message? Also, what command are you using to run in parallel?

renyun0511 November 10, 2011 19:20
hi, Dhruv and danishdude,
I am with the same problem when I use MRFSimpleFoam (OpenFOAM-1.5-dev) in parallel running. The command and steps I adopted are:
http://www.cfd-online.com/Forums/ope...lel-error.html
Here is the information of this error:
Quote:
ibnode1:/public/home/test/ry/OpenFOAM/1.0 # mpirun -np 4 MRFSimpleFoam -parallel
Starting time loop
Creating ggi check
Time = 1
smoothSolver: Solving for Ux, Initial residual = 1, Final residual = 0.0366575, No Iterations 2
smoothSolver: Solving for Uy, Initial residual = 1, Final residual = 0.0436506, No Iterations 2
smoothSolver: Solving for Uz, Initial residual = 1, Final residual = 0.0366069, No Iterations 2
[ibnode1:15759] *** Process received signal ***
[ibnode1:15759] Signal: Floating point exception (8)
[ibnode1:15759] Signal code: (-6)
[ibnode1:15759] Failing at address: 0x3d8f
[ibnode1:15759] [ 0] /lib64/libc.so.6(+0x329e0) [0x7fa88afa29e0]
[ibnode1:15759] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x7fa88afa2945]
[ibnode1:15759] [ 2] /public/software/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPDebug/libOpenFOAM.so(_ZN4Foam6sigFpe13sigFpeHandlerEi+0x aa) [0x7fa88c126760]
[ibnode1:15759] [ 3] /lib64/libc.so.6(+0x329e0) [0x7fa88afa29e0]
[ibnode1:15759] [ 4] /public/software/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPDebug/libOpenFOAM.so(_ZN4Foam6divideERNS_5FieldIdEERKdRK NS_5UListIdEE+0x6b) [0x7fa88c06906c]
[ibnode1:15759] [ 5] MRFSimpleFoam(_ZN4Foam6divideINS_12fvPatchFieldEEE vRNS_10FieldFieldIT_dEERKdRKS4_+0x52) [0x459822]
[ibnode1:15759] [ 6] MRFSimpleFoam(_ZN4Foam6divideINS_12fvPatchFieldENS _7volMeshEEEvRNS_14GeometricFieldIdT_T0_EERKNS_11d imensionedIdEERKS6_+0x76) [0x4598ba]
[ibnode1:15759] [ 7] MRFSimpleFoam(_ZN4FoamdvINS_12fvPatchFieldENS_7vol MeshEEENS_3tmpINS_14GeometricFieldIdT_T0_EEEERKNS_ 11dimensionedIdEERKS8_+0x374) [0x45db48]
[ibnode1:15759] [ 8] MRFSimpleFoam(_ZN4FoamdvINS_12fvPatchFieldENS_7vol MeshEEENS_3tmpINS_14GeometricFieldIdT_T0_EEEERKdRK S8_+0x38) [0x45dc26]
[ibnode1:15759] [ 9] MRFSimpleFoam() [0x43169e]
[ibnode1:15759] [10] /lib64/libc.so.6(__libc_start_main+0xe6) [0x7fa88af8ebc6]
[ibnode1:15759] [11] MRFSimpleFoam() [0x42fa29]
[ibnode1:15759] *** End of error message ***
[ibnode1:15758] *** Process received signal ***
[ibnode1:15758] Signal: Floating point exception (8)
[ibnode1:15758] Signal code: (-6)
[ibnode1:15758] Failing at address: 0x3d8e
[ibnode1:15757] *** Process received signal ***
[ibnode1:15757] Signal: Floating point exception (8)
[ibnode1:15757] Signal code: (-6)
[ibnode1:15757] Failing at address: 0x3d8d
[ibnode1:15758] [ 0] /lib64/libc.so.6(+0x329e0) [0x7f874dde39e0]
[ibnode1:15758] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x7f874dde3945]
[ibnode1:15758] [ 2] /public/software/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPDebug/libOpenFOAM.so(_ZN4Foam6sigFpe13sigFpeHandlerEi+0x aa) [0x7f874ef67760]
[ibnode1:15758] [ 3] /lib64/libc.so.6(+0x329e0) [0x7f874dde39e0]
[ibnode1:15758] [ 4] /public/software/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPDebug/libOpenFOAM.so(_ZN4Foam6divideERNS_5FieldIdEERKdRK NS_5UListIdEE+0x6b) [0x7f874eeaa06c]
[ibnode1:15758] [ 5] MRFSimpleFoam(_ZN4Foam6divideINS_12fvPatchFieldEEE vRNS_10FieldFieldIT_dEERKdRKS4_+0x52) [0x459822]
[ibnode1:15758] [ 6] MRFSimpleFoam(_ZN4Foam6divideINS_12fvPatchFieldENS _7volMeshEEEvRNS_14GeometricFieldIdT_T0_EERKNS_11d imensionedIdEERKS6_+0x76) [0x4598ba]
[ibnode1:15758] [ 7] MRFSimpleFoam(_ZN4FoamdvINS_12fvPatchFieldENS_7vol MeshEEENS_3tmpINS_14GeometricFieldIdT_T0_EEEERKNS_ 11dimensionedIdEERKS8_+0x374) [0x45db48]
[ibnode1:15758] [ 8] MRFSimpleFoam(_ZN4FoamdvINS_12fvPatchFieldENS_7vol MeshEEENS_3tmpINS_14GeometricFieldIdT_T0_EEEERKdRK S8_+0x38) [0x45dc26]
[ibnode1:15758] [ 9] MRFSimpleFoam() [0x43169e]
[ibnode1:15758] [10] /lib64/libc.so.6(__libc_start_main+0xe6) [0x7f874ddcfbc6]
[ibnode1:15758] [11] MRFSimpleFoam() [0x42fa29]
[ibnode1:15758] *** End of error message ***
[ibnode1:15757] [ 0] /lib64/libc.so.6(+0x329e0) [0x7fb116bd99e0]
[ibnode1:15757] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x7fb116bd9945]
[ibnode1:15757] [ 2] /public/software/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPDebug/libOpenFOAM.so(_ZN4Foam6sigFpe13sigFpeHandlerEi+0x aa) [0x7fb117d5d760]
[ibnode1:15757] [ 3] /lib64/libc.so.6(+0x329e0) [0x7fb116bd99e0]
[ibnode1:15757] [ 4] /public/software/OpenFOAM/OpenFOAM-1.5-dev/lib/linux64GccDPDebug/libOpenFOAM.so(_ZN4Foam6divideERNS_5FieldIdEERKdRK NS_5UListIdEE+0x6b) [0x7fb117ca006c]
[ibnode1:15757] [ 5] MRFSimpleFoam(_ZN4Foam6divideINS_12fvPatchFieldEEE vRNS_10FieldFieldIT_dEERKdRKS4_+0x52) [0x459822]
[ibnode1:15757] [ 6] MRFSimpleFoam(_ZN4Foam6divideINS_12fvPatchFieldENS _7volMeshEEEvRNS_14GeometricFieldIdT_T0_EERKNS_11d imensionedIdEERKS6_+0x76) [0x4598ba]
[ibnode1:15757] [ 7] MRFSimpleFoam(_ZN4FoamdvINS_12fvPatchFieldENS_7vol MeshEEENS_3tmpINS_14GeometricFieldIdT_T0_EEEERKNS_ 11dimensionedIdEERKS8_+0x374) [0x45db48]
[ibnode1:15757] [ 8] MRFSimpleFoam(_ZN4FoamdvINS_12fvPatchFieldENS_7vol MeshEEENS_3tmpINS_14GeometricFieldIdT_T0_EEEERKdRK S8_+0x38) [0x45dc26]
[ibnode1:15757] [ 9] MRFSimpleFoam() [0x43169e]
[ibnode1:15757] [10] /lib64/libc.so.6(__libc_start_main+0xe6) [0x7fb116bc5bc6]
[ibnode1:15757] [11] MRFSimpleFoam() [0x42fa29]
[ibnode1:15757] *** End of error message ***
[ibnode1:15753] [0,0,0] ORTE_ERROR_LOG: Timeout in file base/pls_base_orted_cmds.c at line 275
[ibnode1:15753] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line 1166
[ibnode1:15753] [0,0,0] ORTE_ERROR_LOG: Timeout in file errmgr_hnp.c at line 90
mpirun noticed that job rank 2 with PID 15758 on node ibnode1 exited on signal 8 (Floating point exception).
1 additional process aborted (not shown)
[ibnode1:15753] [0,0,0] ORTE_ERROR_LOG: Timeout in file base/pls_base_orted_cmds.c at line 188
[ibnode1:15753] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line 1198
--------------------------------------------------------------------------
mpirun was unable to cleanly terminate the daemons for this job. Returned value Timeout instead of ORTE_SUCCESS.
--------------------------------------------------------------------------
How can you solve this problem?

Yun Ren
regards,
Jiangsu University, China

idrama November 25, 2011 05:06
I only can speculate, but the final residual of Ux etc. are a bit to coarse. Adjust the linear solver setting in order to obtain a better residual. Probably, this might solve your problem. I dosent seems to be mpi problem.

Cheers


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